choose_a: Suggests unit cell side, a, based on atom content

Description Usage Arguments Value Examples

View source: R/direct_space.R

Description

The unit cell side is roughly calculated by adding two times the half-width of the widest gaussian atom to the largest inter-atomic distance. The half-width of the largest gaussian is computed as Ma times the gaussian sigma. If the "P-1" symmetry is present, D is doubled.

Usage

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choose_a(Z, D, SG = "P1", k = ksigma, Ma = 5)

Arguments

Z

A vector of atom Z numbers.

D

A real number. The distance between the two furthest atoms in the cell.

SG

2-letters character string. Symmetry. There are only two symmetries possible when working within 1D crystallography, P1 (no symmetry)and P-1 (inversion through the origin). SG can be either "P1" or "P-1" for this function.

k

A real number. It controls the standard deviation of the gaussian function describing the atom and, thus, the shape of the associated peak. The standard deviation sigma is given by: sigma = k * sqrt(Z)

Ma

A real number. Each gaussian atom has tails truncated at a distance of Ma * sigma from its peak.

Value

A real number that suggests a feasible unit cell side containing all atoms.

Examples

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# 2 carbon atoms, a sulphur and an oxygen
Z <- c(6,8,16,6)

# Distance between the two carbons is 15 angstroms
D <- 15
a <- choose_a(Z,D)

jfoadi/crone documentation built on May 17, 2017, 7:19 p.m.